Systems and user interface for collecting a data set in a flow cytometer

ABSTRACT

Systems in a flow cytometer having an interrogation zone and illumination impinging the interrogation zone include: a lens subsystem including a collimating element that collimates light from the interrogation zone, a light dispersion element that disperses collimated light into a light spectrum, and a focusing lens that focuses the light spectrum onto an array of adjacent detection points; a detector array, including semiconductor detector devices, that collectively detects a full spectral range of input light signals, in which each detector device detects a subset spectral range of the full spectral range of light signals; and a user interface that enables a user to create a set of virtual detector channels by grouping detectors in the detector array, such that each virtual detector channel corresponds to a detector group and has a virtual detector channel range including the sum of subset spectral ranges of the detectors in the corresponding detector group.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Nos.61/406,251 entitled “Detection system for a flow cytometer” and filed 25Oct. 2010, 61/406,255 entitled “Optical and detection system for a flowcytometer” and filed 25 Oct. 2010, and 61/406,259 entitled “Userinterface for a detection system in a flow cytometer” filed 25 Oct.2010, which are each incorporated in its entirety by this reference.

TECHNICAL FIELD

This invention relates generally to the flow cytometer field, and morespecifically to a new and useful systems and user interface in the flowcytometer field.

BACKGROUND

In a flow cytometer, light is directed onto a stream of sample fluidsuch that the light impinges and typically excites particles in thesample, causing the excited particles to emit light. The detection ofthe emitted light provides data that can be analyzed for characterizingthe particles and the sample fluid, such as count, physical structure,chemical structure, and other useful information in applications such asfor research and clinical purposes. The detection system is therefore acrucial component of a flow cytometer and is a factor in not only thequality (e.g., sensitivity, bandwidth) of the collected data, but alsothe overall structure and cost of the complete flow cytometer system. Inconventional flow cytometers, the detection system includesphotomultiplier tubes, or PMTs, which have relatively high sensitivityand high bandwidth, and produces data with relatively low noise.However, PMTs have several disadvantages, such as being relativelyexpensive and exhibiting temperature drift.

Furthermore, a typical flow cytometer detector has a limited collectionrange. In simple terms, the collection range of a typical flow cytometeris smaller than the signal range of the objects being analyzed with theflow cytometer. For this reason, the typical detector is supplied with again level and/or amplifier. Detectors typically collect data relativeto an object's size (light scatter) or brightness (fluorescence); bothtypes of data are often collected on each object detected in the sample.To collect signals from small or faint objects, the gain level isincreased. With an increased gain level, however, the signals from largeor bright objects are too intense to be collected. To collect signalsfrom large or bright objects, the gain level is decreased. With adecreased gain level, however, the signals from small or faint objectsare too weak to be collected. The setting of gain level and otherparameters is complicated and difficult. The limitations of the userinterface of typical flow cytometer systems have several disadvantages,including: (1) the expenditure of valuable user time spent on thegain-setting process to ensure it is set correctly; (2) the requirementof significantly more sample to determine the proper gain settings; (3)the potential loss of valuable data because at least a portion of inputsignals are outside of the user-set “active” dynamic collection rangeand are therefore not collected, and (4) the inability to observe and“undo” changes in user-set gain/scaling settings without runningadditional samples.

The use of detectors in flow cytometers is also complicated by complexoptical systems. To use a conventional optical system, beam splittersand filters must be arranged in a very particular order to properlydirect light of particular wavelengths to the appropriate detectors.Rearrangement of the optical system is required whenever a differentwavelength detection configuration is required, such as experiments ortests using different fluorochromes. A user must skillfully perform thisrearrangement, or the detector system will not function correctly. Thislimitation prevents the easy swapability of the filters and the easymodification of detection parameters. Further, the particulararrangement of the optical system decreases the reliability and theruggedness of the flow cytometers, since alignment of the variousoptical components affects the operability of the detection system.

Thus, there is a need in the flow cytometry field to create new anduseful systems and user interface. This invention provides such new anduseful systems and user interface for collecting a data set in a flowcytometer.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a schematic of the optical system of a preferred embodiment;

FIG. 2 is a schematic of a signal processing circuit for the detectionsystem of a preferred embodiment;

FIG. 3 is a schematic of the detection system and virtual detectorchannels of preferred embodiments;

FIGS. 4A and 4B are flowcharts of a method for collecting a data set,enabled by the user interface of first and second preferred embodiments,respectively;

FIGS. 5A-5E are schematics of variations of a method for collecting adata set, enabled by the user interface of the first preferredembodiment; and

FIGS. 6A-6F are schematics of variations of a method for collecting adata set, enabled by the user interface of the second preferredembodiment.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

The following description of preferred embodiments of the invention isnot intended to limit the invention to these preferred embodiments, butrather to enable any person skilled in the art to make and use thisinvention.

In a preferred embodiment, systems for collecting a data set in a flowcytometer include optical and detection systems in a flow cytometer 102having a flow channel with an interrogation zone and an illuminationsource that impinges the interrogation zone from a particular direction.As shown in FIG. 1, the optical system 100 preferably includes a lenssubsystem including a collimating element that receives and collimateslight from the interrogation zone, a light dispersion element thatdisperses the collimated light into a continuous wavelength spectrum oflight, and a focusing lens that focuses light spectrum onto an array ofadjacent detection points. The detection system 200 for a flow cytometerincludes at least one semiconductor detector device that detects thefocused light at a detection point and produces a signal correspondingto the detected light; a low noise amplifier circuit that amplifies thesignal and is characterized by a high gain-bandwidth product; and anoise filter that reduces electronic noise from the amplified signal.The detection system 200 preferably includes multiple such detectors ina detector array that collectively detects a full spectral range ofinput signals from the flow cytometer, in which each detector detects asubset spectral range of the full spectral range. The user interface 300of a preferred embodiment enables a user to create a set of virtualdetector channels by grouping detectors in the detector array, such thateach virtual detector channel corresponds to a detector group and has avirtual detector channel range including the sum of subset spectralranges of the detectors in the corresponding detector group.

The systems and user interface of the preferred embodiments eliminatethe discrete and complex system of detectors and filters used inconventional flow cytometers, thereby simplifying the overall flowcytometer system and enabling a more compact, easier to use flowcytometer. The optical and detection systems also capture all usablelight, thereby increasing the power and usability of the flow cytometer.Although the optical and detection systems and user interface arepreferably integrated in a flow cytometer, the systems and userinterface may alternatively be used in microscopy and/or any suitableapparatus or application for collecting and detecting light.

Optical System

As shown in FIG. 1, the optical system 100 preferably includes a lenssubsystem including a collimating element 110 that receives andcollimates light from the interrogation zone, a light dispersion element120 that disperses the collimated light into a continuous wavelengthspectrum of light, and a focusing lens 130 that focuses light spectrumonto an array of adjacent detection points 132, such that a detectorarray may collect the focused light at the adjacent detection points132. The optical system 100 may further include a clean-up element thatreduces spurious reflections and/or other undesired optical artifacts.In one embodiment, the optical system 100 receives and directs lighttowards a detection system that includes photodiode light detectors, butmay alternatively receive and direct light toward a detection systemthat includes phototransistor light detectors, or any suitable detector.

The lens subsystem includes multiple lens and/or lens surfaces thatfunction to manipulate the light from the illumination source into aform and/or to detection point locations where the light is detectableby a detector array. In a first stage of the lens subsystem, thecollimating element 110 is preferably a collimating lens that alignslight from the interrogation zone, and more preferably an achromaticdoublet lens, but may include any suitable combination of lenses orother collimating element. The collimating element 110 preferablyperfectly or near-perfectly collimates the light into substantiallyparallel light rays, since the effects of imperfect collimation appearat subsequent stages of the lens subsystem, resulting in poorly-focusedlight at the detection points 132 and thereby degrading the detection ofthe light originating from the interrogation zone. As shown in FIG. 1,the collimating element 110 may be coupled to or otherwise opticallypaired with an aplanatic meniscus lens 112. The pairing of thecollimating element 110 and aplanatic meniscus lens 112 increases theeffective numerical aperture of the first stage of the lens subsystem,thereby increasing the overall efficiency of light collection from theinterrogation zone. The pairing also reduces the overall focal length ofthe first stage of the lens subsystem, without introducing additionalundesirable spherical aberrations or other optical aberrations, whichenables the lens subsystem to be made more compact. In one exemplaryembodiment, the collimating element 110 is an achromatic doublet lenswith an effective focal length of approximately 30 millimeters and theaplanatic meniscus lens has an approximately 50 degree cone, such thatthe triplet lens combination of the collimating element and meniscuslens has an effective focal length of approximately 20 millimeters.

In a second stage of the lens subsystem, the light dispersion element120 functions to disperse the collimated light from the collimatingelement 110 into a continuous wavelength spectrum of light. The lightdispersion element 120 is preferably mounted in alignment with theoutput of the collimating element, such as in a frame, and may bepermanently fixed or adjustable in position relative to the collimatingelement. As shown in FIG. 1, after passing through the light dispersionelement 120, the light is preferably redirected such that light rays ofthe same wavelength are parallel and light rays of different wavelengthsare nonparallel at relative angles corresponding to their relativeposition in the wavelength spectrum. The light dispersion element 120 ispreferably one of multiple variations. In a first variation, the lightdispersion element 120 includes a diffraction grating that splits anddiffracts light into a continuous spectrum of light rays towards thethird stage of the lens subsystem. In a second variation, the lightdispersion element 120 includes a dispersive prism that breaks up thecollimated light into a continuous spectrum of light rays towards thethird stage of the lens subsystem. In either variation, the dispersedlight may follow a fold angle that is an acute angle, which may enable amore compact lens subsystem, or any suitable angle. In an exemplaryembodiment, the light dispersion element 120 is a diffraction grating orprism with a grating of approximately 600 lines/millimeter, and thelight dispersion element provides a fold angle of approximately 22degrees. However, the light dispersion element may include any suitablestructure with any suitable level of grating and/or fold angle.

In a third stage of the lens subsystem, the focusing lens 130 functionsto focus the dispersed, continuous spectrum of light onto an array ofadjacent detection points 132. As shown in FIG. 1, the focusing lens 130preferably gathers light of similar wavelength together such that alllight focused on the array of detection points 132 is arranged inspectral order, but the dispersed light may be focused in any suitablemanner. For example, beam splitters or additional stages in the lenssubsystem may redirect selected spectral portions of the dispersed lightto be arranged in any suitable spectral order, and/or focus selectedspectral portions of the dispersed light onto detection points in anysuitable location. Each detection point 132 may have a spot size ofapproximately 0.8 mm², or any suitable spot size. The array of detectionpoints 132 is preferably a linear array. For instance, lightcorresponding to shorter wavelengths is preferably focused near a firstend of the array of detection points 132, and light corresponding tolonger wavelengths is preferably focused near a second end of the arrayof detection points 132, opposite the first end. However, the array ofdetection points may alternatively be an arcuate array (e.g., an openarc segment or enclosed circle or ellipse) or any suitable shape. In anexemplary embodiment, the focusing lens 130 has an effective focallength of approximately 160 millimeters and focuses the light to alinear array of detection points covering a dispersion distance ofapproximately 43 millimeters long. However, the focusing lens may be anysuitable lens or lens surface, and may focus the light to any suitablearrangement of detection points.

In some embodiments, the optical system 100 may further include aclean-up element 140 that functions to reduce undesired opticalartifacts or other aspects of the received light, such as crosstalk fromspurious grating reflections. In one variation, the clean-up element 140includes an optical filter. For example, the optical filter may becontinuously variable, segmented, upper half, lower half, or anysuitable type of filter. The filter may additionally and/oralternatively block one or more specific wavelengths from reaching thearray of detector points 132, such as the wavelength of a laser orlasers used to excite fluorescent particles in the interrogation zone.For example, such a Mocking filter may include an optical notch filter,or a thin Mocking bar that positioned at a particular detection point toabsorb a particular wavelength or mask the detector from receiving lightof the particular wavelength at the detection point, but the Mockingfilter may additionally and/or alternatively include any suitablefiltering device. In another variation, the clean-up element 140includes a slit grid, which may include any suitable slit grid known toone ordinarily skilled in the art or other suitable slit grid. Theoptical system may include any suitable number of clean-up elements 140.One or more clean-up elements 140 may be positioned after the lightdispersion stage of the lens subsystem and before or after the focusingstage of the lens subsystem, or in any suitable portion of the lenssubsystem.

Detection System

The detection system 200 preferably includes one or more semiconductorlight detector devices 212 in a detector array 210. Each semiconductordetector device 212 detects the light at a respective detection point132 (focused by the optical system 100 described above, or any suitableoptical system) and produces an electrical signal corresponding to thedetected light. As shown in FIG. 2, the detection system 200 preferablyfurther includes signal processing circuitry including: a low noiseamplifier circuit 220 that boosts or amplifies the signal from thedetector device 212 and that is characterized by a high gain-bandwidthproduct; and a noise filter 230 that reduces electronic noise from theamplified signal.

The semiconductor detector device 212 functions to convert light into anelectrical signal having characteristics that correlate with the natureof the light received from the interrogation zone. The wavelengthsensitivity of the detector device 212 is preferably optimized to detectlight between a full range of approximately 400 nanometers and 900nanometers in wavelength, either a subset of the full range or over theentire full range. Furthermore, the wavelength sensitivity of thedetector device 212 may be optimized to minimize detection of light inthe infrared range, such as to avoid responding to sources of heat inthe flow cytometer or other instrument in which the detection system isintegrated. However, the detector devices may be optimized to detect anysuitable range of wavelengths of light.

The angular sensitivity of the semiconductor detector device 212 may beoptimized to receive light in a cone approximately corresponding to thefocused cone of light emanating from the light focusing element of theoptical system described above, while rejecting stray light passingoutside of the cone, which may thereby minimize sensitivity to lighttraveling off-axis within the optical system. Furthermore, thesemiconductor detector device 212 may be shielded from any backlight orother ambient light sources to minimize background noise in the signaland improve the accuracy of the resulting collected data set from theflow cytometer (or other instrument). The semiconductor device 212 mayadditionally and/or alternatively be shielded from electromagneticfields to minimize induced electronic noise. Furthermore, thesemiconductor detector device 212 may include temperature compensationto minimize any temperature-induced changes in gain or linearity of theoutput signal.

The semiconductor detector device 212 may be any suitable semiconductordevice or light detector device. In a preferred variation, thesemiconductor detector device 212 is a photodiode, and more preferably aPIN photodiode, although the photodiode may be any suitable kind ofdiode. The photodiode preferably has a very low capacitance, such asapproximately 20 pF or less. Since photodiodes with low capacitance aregenerally physically smaller and have a smaller light-sensitive region,the photodiode detector devices 212 are preferably placed at detectionpoints 132 at which light is well-focused, such as by the optical systemdescribed above or any suitable optical system. The photodiode ispreferably configured to output current that correlates withcharacteristics of the received light, but may alternatively beconfigured to output another suitable electrical characteristic, such asvoltage.

In an alternative variation, the semiconductor detector device 212 is aphototransistor. Like the photodiode of the preferred variation, thephototransistor preferably has a very low capacitance and may have asmall light-sensitive region such that the phototransistor requiresplacement at a detection point receiving well-focused light. Thephototransistor may be configured to provide an output signal having asubstantially linear gain response across the intended light power rangeof the input signals, such as by applying a suitable current bias to thebase of the phototransistor, typically in the range of approximately 10μm to 1 mA. Furthermore, the output signal from the phototransistor maybe converted from a current signal to a voltage signal, such as byfeeding the output signal into the low-noise amplifier circuit, a loadresistor or other suitable circuitry components. In some embodiments,the phototransistor may provide additional current gain that may beleveraged to increase gain of the signal and/or increase thesignal-to-noise ratio. In particular, the use of a phototransistor mayreduce the required resistance value of the gain resistor in theamplifier circuit, and consequently may reduce the thermal noisecontribution to overall detector noise.

The low-noise amplifier circuit 220 functions to convert current inputfrom the semiconductor detector device 212 to a voltage output and toamplify the signal from the semiconductor detector device 212. Thelow-noise amplifier circuit 220 preferably includes a transimpedanceamplifier, but may be any suitable kind of amplifier. The amplifiercircuit preferably has a high open-loop gain-bandwidth product, such asapproximately 1 GHz or more. The combination of a semiconductor detectordevice 212 having low capacitance and a transimpedance amplifier havinga high gain-bandwidth product may enable the detection system 200 tohave high gain (to amplify the signal from the detector) whilemaintaining high sensitivity and high bandwidth. The amplifier circuit220 may further be characterized with a high feedback resistance, lowvoltage noise and low current noise to reduce overall noise in thesignal, and low input capacitance. In an exemplary embodiment, thetransimpedance amplifier has a feedback resistance between 1-20 MOhmsand preferably more than approximately 10 MOhms, voltage noise of lessthan approximately 5 nV/rtHz, current noise of less than approximately 5fA/rtHz, and input capacitance less than approximately 6 pF. However,other embodiments of the amplifier circuit may have any suitablespecifications. The amplifier circuit 220 may additionally and/oralternatively include any suitable electronic components that performcurrent-to-voltage conversion, or the detection system may include anysuitable conversion circuitry (e.g., a passive current-to-voltageconverter). The amplifier circuit may additionally and/or alternativelyinclude digital signal processing.

The noise filter 230 functions to reduce electronic noise and/orphoton-induced noise from the amplified signal, thereby increasing thesignal-to-noise ratio. The noise filter 230 may include a low passfilter that quickly attenuates higher frequency noise above apredetermined cutoff point. The noise filter 230 may be implemented inhardware circuitry and/or digitally. In an exemplary embodiment, the lowpass filter includes 120 dB or better attenuation, preferably with a 500kHz or smaller transition band. The noise filter may additionally and/oralternatively include further signal processing techniques such as asmoothing algorithm.

As shown in FIG. 3, in a preferred embodiment, the detection system 200preferably includes multiple semiconductor light detector devices 212 ina detector array 210 that collectively detects a full spectral range 250of input signals from the flow cytometer, and in which each detectordetects a subset spectral range 252 of the full spectral range. However,the semiconductor detector device 212 (e.g. photodiode or phototransistor) may alternatively be used in any suitable detection system.In an exemplary embodiment, the detection system detects a full spectralrange 250 of input signals of approximately 400-900 nm, but mayalternatively detect any suitable spectral range of light. Overall, thedetection system 200 preferably is configured to have a bandwidth of atleast approximately 400 kHz. However, in some embodiments, such as foruse in flow cytometers having frequency modulated lasers at lightsources in the interrogation zone, the detection system 200 may have abandwidth of at least approximately 2 MHz. Alternatively, the detectionsystem 200 may have any suitable bandwidth. Furthermore, the detectorarray 210 preferably detects a wide range of input signals that includesat least a 1:100,000 ratio, and more preferably at least a 1:1,000,000ratio, between the faintest objects and the brightest objects. In apreferred embodiment, the detector array 210 is a linear array, suchthat a dispersed spectrum of light may be incident on the detectorarray, with light of shorter wavelengths detected near a first end ofthe linear array and light of longer wavelengths detected near a secondend of the linear array opposite the first end. Alternatively, thedetector array 210 may be an arcuate array (e.g., an open arc segment orenclosed circle or ellipse) or any suitable shape, preferably withadjacent and contiguous detector devices 212.

Each detector device 212 in the detector array 210 preferably detects arespective portion or subset of the full spectral range 250 of thedetection system 200. In particular, the detector array 210 ispreferably capable of detecting a continuous spectral range of light,and each detector device 212 may be configured to detect a subsetspectral range based on its individual characteristics, and/or by itsrelative position in the detector array 210. For example, the detectorarray 210 may include 50 detectors that each detects light ofapproximately 10 nm wavelength increments, from approximately 400-900nm. The subset spectral ranges 252 of the detectors 212 may be of equalspan (e.g. each detector detects, as a result of capability and/orrespective position in the detector array, a subset range of 10 nm inthe full spectral range), or may be of unequal span. In someembodiments, some or all of the detectors may detect light ofoverlapping spectra. For example, one detector may detect light of510-530 nm, and an adjacent detector may detect light of 520-540 nm,such that the two adjacent detectors both detect light of 10 nm (520-530nm). However, the detector array 210 may include any suitable number ofdetectors, and the detectors may detect any suitable wavelength rangesof light and/or overlapping wavelength ranges of light. The “spillover”spectral overlap resulting from detection of a particular wavelength oflight by multiple detectors may be automatically compensated bytechniques known and used by one ordinarily skilled in the art,compensated by user-controlled techniques, and/or any suitablecompensation methods. Although the detector array 210 preferably detectsa continuous spectral range of light, the detector array mayalternatively detect a discontinuous spectral range of light, orselected subsets of the full spectral range 250 of light.

As shown in FIG. 3, individual detectors may be grouped into virtualdetector channels 240, and/or actual detector channels, through whichthe data set from the flow cytometer or other instrument may becollected. Each virtual detector channel 240 corresponds to a detectorgroup and has a virtual detector channel range 242 that includes the sumof the subset spectral ranges 252 of the detectors in the correspondingdetector group. In other words, each virtual detector channel 240includes the summed or combined input signals collectively detected bythe individual detectors 212 in the detector group corresponding to thevirtual detector channel 240. Some or all of the virtual detectorchannels may include substantially equal virtual detector channel rangesor unequal virtual detector channel ranges. In particular, the detectorsmay be grouped in a first configuration corresponding to a first set ofvirtual detector channels 240 and in a second configurationcorresponding to a second set of virtual detector channels 240, wherethe first and second configurations are different. In other words, thegrouping of signals from the detectors may be arranged and repeatedlyrearranged in different groups between uses and applications, withoutrequiring physical rearrangement of the components of the optical systemand detection system.

User Interface

The user interface 300 for a flow cytometer is used to enable thegrouping of detector signals to form virtual detector channels throughwhich data is collected and organized. As shown in FIGS. 4A and 4B, inpreferred embodiments, the user interface 300 provides a method forcollecting a data set for a flow cytometer sample in a flow cytometerincluding the steps of: providing a detector array S310 having aplurality of detectors that collectively detect a full spectral range ofinput signals from the flow cytometer, in which each detector detects asubset spectral range of the full spectral range; creating a set ofvirtual detector channels S320 by grouping detectors in the detectorarray, and collecting the full spectral range of input signals S370 fromthe flow cytometer sample with the detector array. Each virtual detectorchannel corresponds to a detector group and has a virtual detectorchannel range that includes the sum of subset spectral ranges of thedetectors in the corresponding detector group. The step of creating aset of virtual detector channels S320, which may include one or more ofseveral variations of substeps, may be performed before and/or after thestep of collecting input signals S370. The method may further includestoring an initial data set based on the collected input signals S380and/or storing a configuration file of the configuration of the virtualdetector channels S390. The user interface 300 enables extraction ofdata from a flow cytometer system having the optical and/or detectionsystems as described above, or any suitable instrument having an arrayof multiple detectors that each detects a portion of a full spectrum oflight input signals. The user interface 300 enables a more comprehensivecollection of data, and simplifies the process for setting up andconfiguring the detector system of the flow cytometer. However, the userinterface and method for collecting a data set may alternatively be usedin any suitable system requiring detection of a substantial spectrum ofsignals, such as microscopy.

The step of providing a detector array S310 preferably includesproviding a system that detects known subsets of an entire light (e.g.,fluorescence) spectrum detected by the flow cytometer. The detectorarray is preferably similar to the detection system described above andshown in FIGS. 2 and 3, but may alternatively be any suitable detectionsystem. In particular, the detector array includes separate individualdetector devices that detect a dispersed full spectrum of light suchthat adjacent detectors may detect portions or subset spectral ranges ofthe full spectrum of light, and more preferably such that adjacentdetectors detect contiguous subset spectral ranges of the full spectrumof light. For example, within a group of adjacent detectors in thedetector array, each detector may detector light in 10 nm increments,such that a first detector may detect light having a wavelength ofapproximately 491-500 nm, a second middle detector may detect lighthaving a wavelength of approximately 501-510 nm, and a third detectormay detect light having a wavelength of approximately 511-521 nm. Thedetector array may include photodiodes, phototransistors, or anysuitable kind of light detector.

The step of creating a set of virtual detector channels S320 functionsto organize the signals collected by detectors in the detector arrayinto designated data channels. As best shown in FIG. 3, creating a setof virtual detector channels S320 includes grouping detectors in thedetector array S322. Each virtual detector channel 240 corresponds to adetector group and has a virtual detector channel range that includesthe sum of the subset spectral ranges of the detectors in thecorresponding detector group. In other words, each virtual detectorchannel 240 includes the summed or combined input signals collectivelydetected by the individual detectors in the detector group correspondingto the virtual detector channel. One or more detector groups may includedetectors that are physically contiguous with each other (e.g., a“block” of detectors and/or detect contiguous subset spectral ranges oflight, such that the corresponding virtual detector channel rangecollects light of a continuous spectral range (as in virtual detectorchannels 240 a, 240 b, and 240 d). Furthermore, one or more detectorgroups may include detectors that are not physical contiguous with each(e.g., a “split block” of detectors) and/or detect not contiguous subsetspectral ranges of light, such that the corresponding virtual detectorchannel range collects light of a discontinuous spectral range, as invirtual detector channel 240 c.

The step of collecting the full spectral range of input signals S370functions to gather raw data with the detector array. Collecting inputsignals S370 may include collecting a full dynamic range of inputsignals that provides at least a 1:100,000 ratio, and more preferably atleast a 1:1,000,000 ratio, between the faintest signals and thebrightest signals from the flow cytometer sample. In a preferredembodiment, the data is collected in a raw, unmodified format withoutadjustment in gain level of the detectors, but may be collected in anysuitable manner.

As shown in FIGS. 5 and 6, the step of creating a set of virtualdetector channels S320 may be performed before and/or after the step ofcollecting input signals S370, such as before and/or after performing asample run on the flow cytometer. In a first preferred embodiment, thestep of creating a set of virtual detector channels S320 is performedbefore collecting input signals. As shown in FIG. 5A, in a firstvariation of this embodiment, the step of creating a set of virtualdetector channels S320 includes receiving a user selection of detectorgroups S330 in which the user manually enters or indicates detectorgroups that make up the detector channels. For example, each detectormay be labeled or numbered, and the user may specify that detectors “x”through “y” is a detector group. Since each detector is designated fordetecting a particular subset spectrum range of input signals, the userselection of detector groups in turn creates virtual detector channelscorresponding to the detector groups. For a flow cytometer system havingmultiple lasers, the user may further specify which laser is assigned toeach detector, detector group, and/or virtual detector channel.

As shown in FIG. 5B, in a second variation of the first preferredembodiment, the step of creating a set of virtual detector channels S320includes receiving a user selection of desired virtual detector channelranges S340 (or summed subset spectrum ranges of input signals) andgrouping detectors into detector groups that correspond to the selectionof virtual detector channel ranges S342, thereby forming a set ofvirtual detector channels that define the desired virtual detectorchannel ranges. For example, the user may specify a range ofwavelengths, such as that between wavelength “a” and wavelength “b”, toassign to a particular virtual detector channel, and the user interface300 may automatically correlate the range of wavelengths to specificindividual detectors, by determining which individual detectors to grouptogether to form a virtual detector channel that detects light betweenwavelengths “a” and “b”. In some embodiments, the user interface 300 mayautomatically exclude certain detectors from any detector group orvirtual detector channel, such as in scenarios in which lasers in theoptical system are active.

As shown in FIG. 5C, in a third variation of the first preferredembodiment, the step of creating a set of virtual detector channels S320includes receiving one or more configuration parameters S350 andoptimally grouping detectors based on the configuration parameters S352.In an example of this variation, the step of creating a set of virtualdetector channels includes receiving a user selection of a set offluorochromes S354 that tag a flow cytometer sample, determining anoptimal detector group for each fluorochrome based on at least oneconfiguration parameter, and assigning the optimal detector group toeach fluorochrome S356 and thereby providing a virtual detector channelfor each fluorochrome. Between different sample runs and/or sets offluorochromes, the detector groups may be reassigned to providedifferent suitable virtual detector channels for different applications.Optimally grouping detectors S352 may be dependent on one or more ofseveral configuration parameters, including: minimizing spillover(overlapping detection of a fluorochrome between multiple detectorchannels), simplifying requirements for spillover compensation(typically algorithms to compensate for spillover in the data),instrument-specific calibration parameters, maximizing sensitivity ofthe detector channels (such as based on previous sample runs with aparticular set of fluorochromes), any suitable configuration parameterbased on the user-selected set of fluorochromes or instrumentation, orany suitable parameter. Optimally grouping detectors S352 is preferablyperformed automatically by the user interface 300, but may additionallyand/or alternatively be performed manually by the user. The userinterface and/or user may further determine the optical laserconfiguration in the flow cytometer for each fluorochrome.

As shown in FIG. 5D, in a fourth variation of the firs preferredembodiment, the step of creating a set of virtual detector channels S320includes receiving a configuration file S360 that defines apredetermined group of detectors, arrangement of virtual detectorchannels, laser configuration, and/or any suitable settings for the flowcytometer system. In this variation, the step of grouping the detectorspreferably incorporates the settings in the configuration file, and/ormay include further modifications by the user or system. Theconfiguration file may be directly provided by the user such as onportable media, selected from the user interface 300, selected anddownloaded from a network or server, provided in a machine-read samplelabel such as a bar code, or by any suitable means. The configurationfile may be a saved configuration file from a previous sample run fromthe same or different flow cytometer system or other instrument, or maybe a template configuration file. A configuration file defining thevirtual detector channel settings and/or other instrument settings mayhelp increase usability of the instrument, and help ensure consistencyin analysis for similar experiments or tests. This consistency inanalysis for similar experiments or tests may be particularly importantin some applications, such as clinical applications.

In a second preferred embodiment, the step of creating a set of virtualdetector channels S320 is performed after collecting input signals S370(such as after a sample run with the flow cytometer system). As shown inFIGS. 6B and 6C, in first and second variations of this embodiment thestep of creating a set of virtual detector channels S320 includereceiving a user selection of detector groups S330 and receiving a userselection of desired virtual detector channel ranges S340, respectively,similar to the first and second variations of the first preferredembodiment.

As shown in FIG. 6D, in a third variation of this embodiment, the stepof creating a set of virtual detector channels S320 includes receivingone or more configuration parameters S350 and optimally groupingdetectors based on the configuration parameters S352, similar to thethird variation of the first embodiment. Furthermore, the user interface300 may additionally and/or alternatively optimize the detector groupingbased on bright and/or dim (or blank) peaks of a multi-intensity flowcytometer sample, which may be identified automatically by the userinterface and/or manually by the user. This optimization may occur aftera sample run, or after the user runs a set of experimental controls butbefore the actual sample run.

As shown in FIG. 6E, in a fourth variation of the second preferredembodiment, the step of creating a set of virtual detector channels S320includes receiving a configuration file S360, similar to the fourthvariation of the first preferred embodiment.

Although the step of creating a set of virtual detector channels S320 ispreferably one of the above variations, in other embodiments the step ofcreating a set of virtual detector channels S320 may be any suitablecombination or permutation of the above variations and/or any suitableprocesses for forming virtual detector channels. For example, one ormore of the variations of creating a set of virtual detector channels ofthe first embodiment may be implemented in some manner after the step ofcollecting input signals. Similarly, one or more of the variations ofcreating a set of virtual detector channels of the second embodiment maybe implemented in some manner before the step of collecting inputsignals. Furthermore, through the user interface 300 or other means, thevirtual detector channels may be created in multiple configurations fora single sample run (e.g. in a first configuration before collecting theinput signals and in a second configuration, different from the firstconfiguration, after collecting the input signals) and/or betweendifferent instances of sample runs (e.g. in a first configuration forone sample run and in a second configuration, different from the firstconfiguration, for another sample run).

As shown in FIGS. 4-6, the user interface 300 may further enable storingthe collected input signals from most, if not all, available detectors.Storing the collected input signals may include storing an input signalas the signal individually collected by each separate detector in thedetector array S380 (e.g., FIG. 6A), and/or may include storing theinput signal as the signal collected by each separate detector groupthrough the virtual detector channel S380′ (e.g., FIG. 6F). The data setof collected input signals may be saved to a local memory, portablemedia, server, network or any suitable memory. The stored data setpreferably includes the full spectral range of the detectors, but mayinclude any suitable portion of the spectral range or collected signals.The stored data set may also be useful for analysis and othermanipulations, as described in U.S. Pat. No. 7,996,188 entitled “Userinterface for a flow cytometer”, which is incorporated in its entiretyby this reference.

As shown in FIGS. 4-6, the user interface 300 may further enable storinga configuration file S390 that defines a predetermined grouping ofdetectors, arrangement of virtual detector channels, laserconfiguration, and/or any suitable settings for the flow cytometersystem. The step of storing the configuration file S390 may includesaving to a local memory or portable media, saving to a server ornetwork, or any suitable saving step. The stored configuration file maybe used for future sample runs, as described above, and/or as atemplate. Multiple configuration files may be stored. For example, afirst configuration file may be stored immediately after a sample run tosave an initial configuration of detector groups and virtual detectorchannels, and a second configuration file may be stored after optimizingthe grouping based on characteristics of the collected data. In thisexample, the first and second configuration files may be compared oranalyzed for future reference. The user interface 300 may additionallyand/or alternatively include exporting the configuration file to adifferent medium, such as a printout.

As a person skilled in the art will recognize from the previous detaileddescription and from the figures and claims, modifications and changescan be made to the preferred embodiments of the invention withoutdeparting from the scope of this invention defined in the followingclaims.

I claim:
 1. A system for collecting a data set for a flow cytometersample in a flow cytometer, comprising: a detector array, including aplurality of detectors, that collectively detects a full spectral rangeof input signals from the flow cytometer, wherein each detector detectsa subset spectral range of the full spectral range; and a user interfacethat enables a user to create a set of virtual detector channels bygrouping detectors in the detector array, such that each virtualdetector channel corresponds to a detector group and has a virtualdetector channel range including the sum of subset spectral ranges ofthe detectors in the corresponding detector group.
 2. The system ofclaim 1, wherein the plurality of detectors may be grouped in a firstconfiguration corresponding to a first set of virtual detector channelsand in a second configuration corresponding to a second set of virtualdetector channels, wherein the first and second configurations aredifferent.
 3. The system of claim 2, wherein the detector arraycollectively detects a wide range of input signals that includes atleast a 1:1,000,000 ratio between the faintest objects and the brightestobjects.
 4. The system of claim 1, wherein the detector array is alinear array of detectors.
 5. The system of claim 4, wherein the lineararray of detectors includes a plurality of photodiodes.
 6. The system ofclaim 4, wherein the linear array of detectors includes a plurality ofphototransistors.
 7. The system of claim 1, wherein the subset spectralranges of the plurality of detectors are contiguous.
 8. The system ofclaim 1, wherein the subset spectral ranges of the plurality ofdetectors overlap.
 9. The system of claim 1, wherein the detector arraydetects a full spectral range of input signals of approximately 400 nmto 900 nm.
 10. The system of claim 9, wherein the subset spectral rangesof the plurality of detectors are of approximately equal span.
 11. Amethod for collecting a data set for a flow cytometer sample in a flowcytometer, comprising the steps of: providing a detector array having aplurality of detectors that collectively detect a full spectral range ofinput signals from the flow cytometer, wherein each detector detects asubset spectral range of the full spectral range; creating a set ofvirtual detector channels by grouping detectors in the detector array,wherein each virtual detector channel corresponds to a detector groupand has a virtual detector channel range including the sum of subsetspectral ranges of the detectors in the corresponding detector group;and collecting the full spectral range of input signals from the flowcytometer sample with the detector array.
 12. The method of claim 11,wherein collecting input signals includes collecting a wide range ofinput signals that includes at least a 1:1,000,000 ratio between thefaintest objects and the brightest objects.
 13. The method of claim 11,wherein creating a set of virtual detector channels includes receiving auser selection of detector groups.
 14. The method of claim 11, whereincreating a set of virtual detector channels includes receiving a userselection of virtual detector channel ranges and grouping detectors intodetector groups that correspond to the selection of virtual detectorchannel ranges.
 15. The method of claim 11, wherein creating a set ofvirtual detector channels includes receiving at least one configurationparameter and optimally grouping detectors based on the at least oneconfiguration parameter.
 16. The method of claim 15, wherein optimallygrouping detectors based on the configuration parameter includes atleast one of: minimizing spillover between virtual detector channels andmaximizing sensitivity of the virtual detector channels.
 17. The methodof claim 15, wherein creating a set of virtual detector channelsincludes receiving a user selection of a set of fluorochromes andassigning a virtual detector channel for each of the selectedfluorochromes.
 18. The method of claim 11, wherein creating a set ofvirtual detector channels includes receiving a configuration filespecifying virtual detector channel settings.
 19. The method of claim11, wherein creating a set of virtual detector channels is performedbefore collecting input signals.
 20. The method of claim 11, whereincreating a set of virtual detector channels may be performed aftercollecting input signals.
 21. The method of claim 20, further comprisingstoring the collected input signals.
 22. The method of claim 21, whereinstoring the collected input signals includes storing the input signalsas that individually collected by each separate detector in the detectorarray.
 23. The method of claim 21, wherein storing the collected inputsignals includes storing the input signals as that collected by eachseparate virtual detector channel.
 24. The method of claim 11, furthercomprising allowing a user to group the detectors in a firstconfiguration corresponding to a first set of virtual detector channelsand in a second configuration corresponding to a second set of virtualdetector channels, wherein the first and second configurations aredifferent.
 25. An optical and detection system for a flow cytometerhaving a flow channel with an interrogation zone and an illuminationsource that impinges the interrogation zone from a particular direction,the optical system comprising: a lens subsystem including: a collimatingelement that receives and collimates light from the interrogation zone;a light dispersion element that disperses the collimated light into acontinuous wavelength spectrum of light; and a focusing lens thatfocuses the spectrum of light onto an array of adjacent detectionpoints; and a plurality of contiguous detectors that detect light at theadjacent detection points.
 26. The optical system of claim 25, whereinthe collimating element includes an achromatic doublet lens.
 27. Theoptical system of claim 26, wherein the achromatic doublet lens isoptically paired with an aplanatic meniscus lens.
 28. The optical systemof claim 27, wherein the combination of the doublet lens and themeniscus lens has an effective focal length of approximately 20millimeters.
 29. The optical system of claim 25, wherein the lightdispersion element disperses the collimated light with an acute foldangle.
 30. The optical system of claim 29, wherein the light dispersionelement includes a dispersive prism.
 31. The optical system of claim 29,wherein the light dispersion element includes a diffraction grating. 32.The optical system of claim 25, wherein the plurality of contiguousdetectors are arranged in a linear array of detectors.
 33. The opticalsystem of claim 32, wherein the linear array of detectors includes aplurality of photodiodes.
 34. A detection system for a flow cytometerhaving a flow channel with an interrogation zone, an optical system thatcollimates light from the interrogation zone, and a focusing lenssurface that focuses the collimated light to a detection point, thedetection system comprising: a plurality of semiconductor devices thateach detects the focused light at the detection point and produces asignal corresponding to the detected light; a low noise amplifiercircuit that amplifies the signal, wherein the amplifier circuit ischaracterized by a high gain-bandwidth product; and a noise filter thatreduces electronic noise from the amplified signal.
 35. The detectionsystem of claim 34, wherein the plurality of semiconductor devices arearranged in a linear array to detect light at a plurality of adjacentdetection points.
 36. The detection system of claim 34, wherein theplurality of semiconductor devices includes photodiodes.
 37. Thedetection system of claim 36, wherein the photodiode has a capacitanceof approximately 20 pF or less.
 38. The detection system of claim 34,wherein the semiconductor device is a phototransistor.
 39. The detectionsystem of claim 34, wherein the amplifier circuit has an open loopgain-bandwidth product of at least 1 GHz.
 40. The detection system ofclaim 39, wherein the amplifier is a transimpedance amplifier.